Coalescent — Stephen Baxter

When his father dies suddenly, George Poole stumbles onto a family secret: He has a twin sister he never knew existed, who was raised by an enigmatic cult called the Order. The Order is a hive--a human hive with a dominant queen--that has prospered below the streets of Rome for almost two millennia. After Poole enters the Order's vast underground city and meets the disturbing inhabitants, he uncovers evidence that they have embarked on a divergent evolutionary path. These genetically superior humans are equipped with the tools necessary to render modern Homo sapiens as extinct as the Neanderthals. And now they are preparing to leave their underground realm.